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- EMDB-9106: Structure of a group II intron retroelement after DNA integration -

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Basic information

Entry
Database: EMDB / ID: EMD-9106
TitleStructure of a group II intron retroelement after DNA integration
Map datagroup II intron retroelement
Sample
  • Complex: T.el4h group II intron retroelement
    • Other: T.el4h RNA
    • DNA: Sense Target DNA
    • Protein or peptide: Maturase reverse transcriptase
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
Keywordsgroup II intron / retroelement / retrotransposition / RNA-DNA-RNA Binding Protein complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / endonuclease activity / nucleic acid binding / zinc ion binding
Similarity search - Function
Reverse transcriptase, N-terminal domain / N-terminal domain of reverse transcriptase / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / HNH endonuclease / HNH endonuclease / HNH nucleases / : / HNH nuclease ...Reverse transcriptase, N-terminal domain / N-terminal domain of reverse transcriptase / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / HNH endonuclease / HNH endonuclease / HNH nucleases / : / HNH nuclease / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Maturase reverse transcriptase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria) / Thermosynechococcus elongatus (strain BP-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHaack D / Yan X
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM033050 United States
National Institutes of Health/Office of the DirectorDP5 OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM103368 United States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.
Authors: Daniel B Haack / Xiaodong Yan / Cheng Zhang / Jason Hingey / Dmitry Lyumkis / Timothy S Baker / Navtej Toor /
Abstract: Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a ...Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-Å resolution of a group II intron reverse splicing into DNA. These structures reveal that the branch-site domain VI helix swings 90°, enabling substrate exchange during DNA integration. The maturase assists catalysis through a transient RNA-protein contact with domain VI that positions the branch-site adenosine for lariat formation during forward splicing. These findings provide the first direct evidence of the role the maturase plays during group II intron catalysis. The domain VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence for a retroelement origin of the spliceosome.
History
DepositionSep 6, 2018-
Header (metadata) releaseJul 3, 2019-
Map releaseAug 14, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mec
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9106.png

Downloads & links

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Map

FileDownload / File: emd_9106.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgroup II intron retroelement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 316. Å		0.79 Å/pix.
x 400 pix.
= 316. Å		0.79 Å/pix.
x 400 pix.
= 316. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.065666266 - 0.12535165
Average (Standard dev.)0.0002053234 (±0.0026104937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 316.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.790.790.79
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z316.000316.000316.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0660.1250.000

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Supplemental data

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Sample components

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Entire : T.el4h group II intron retroelement

EntireName: T.el4h group II intron retroelement
Components
  • Complex: T.el4h group II intron retroelement
    • Other: T.el4h RNA
    • DNA: Sense Target DNA
    • Protein or peptide: Maturase reverse transcriptase
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION

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Supramolecule #1: T.el4h group II intron retroelement

SupramoleculeName: T.el4h group II intron retroelement / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermosynechococcus elongatus (bacteria)

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Macromolecule #1: T.el4h RNA

MacromoleculeName: T.el4h RNA / type: other / ID: 1 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Thermosynechococcus elongatus (bacteria)
Molecular weightTheoretical: 280.854031 KDa
SequenceString: UUGCGACGCG AAAGCUAGCC AGAUGAUUGU CCCACUAGCC CAACAAGCUA GAACGGGACC GGUUGUUCCC CCAACCGUAG CCUAGGGAG GCAUGCGUGA CUGGUAACGG UCAGGUGUGA AGCCCUCCCG ACAAUGUAGC CCGAACCGCA AGGUUGAAGC U GAAUCCGU ...String:
UUGCGACGCG AAAGCUAGCC AGAUGAUUGU CCCACUAGCC CAACAAGCUA GAACGGGACC GGUUGUUCCC CCAACCGUAG CCUAGGGAG GCAUGCGUGA CUGGUAACGG UCAGGUGUGA AGCCCUCCCG ACAAUGUAGC CCGAACCGCA AGGUUGAAGC U GAAUCCGU GAGGAGGAAG CAACUUCACC AGUGUCAGGU GAUAGGGAAC UAGGCUUGAG GGUAUGGUGA GCACAUGCGA AG UGAUGUC AGAAGCCUCG UCACAGACCA ACAGGCCAAA GACACUGAUA GGCCUGAGCC AAAACGGCAA AUGGAUAGGC UAC AUCGCU CGCUCGUCGG UGUACGGGGA CGUCAAUCCA UCGGGGCACA GUCACCACCU AACCCCUCGU GUCAUCUGGU UGGA ACGCG GUAAGCCCGU AUCCUCGCCU UGAACACUCA AGGCAGGCAA ACCGUAAGGA AUGCUGAUGG GGGUGCGGGU AUGGG AUGC AGGAGAAAGC GAAUGCCGGU CUGUAAUGGA CCGGAUAGGG GUUGAGGAGA CAAUCCAACA UCACCCCGCC CGAAAG GGA GCAGACUUCC UGCUGGUCUC UCUUUGCGAG AUAGCCUGUA GAACCUCUUG AAUGGAGACA AGGCAAAUGG CAGUGGA AC AAACCACUGG UGCGGUCACC AACCAAACGG AAACAAGCUG GCACAGCAUA GACUGGGCCA AAGCCAACCG UGAGGUAA A GAGGCUGCAA GUGCGUAUCG CAAAGGCGUU CGCGCCGGUU CCUCUUGAAA GAGGGGCUUU GAGAGGCCUG AGCCGGAUG UGGGGAAACU CACAAGUCCG GUUCUUAGGG GGCGGGGAUG GCAGUAAUGC CUCCCUGCUA CCCGGCG
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Sense Target DNA

MacromoleculeName: Sense Target DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Thermosynechococcus elongatus (bacteria)
Molecular weightTheoretical: 14.032991 KDa
SequenceString:
(DG)(DA)(DT)(DA)(DG)(DA)(DG)(DA)(DT)(DT) (DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DT) (DT)(DG)(DG)(DC)(DC)(DG)(DA)(DG)(DC) (DG)(DG)(DA)(DT)(DG)(DA)(DG)(DG)(DC)(DA) (DG) (DC)(DG)(DA)(DA)(DC)

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Macromolecule #3: Maturase reverse transcriptase

MacromoleculeName: Maturase reverse transcriptase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1
Molecular weightTheoretical: 65.065121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METRQMAVEQ TTGAVTNQTE TSWHSIDWAK ANREVKRLQV RIAKAVKEGR WGKVKALQWL LTHSFYGKAL AVKRVTDNSG SKTPGVDGI TWSTQEQKAQ AIKSLRRRGY KPQPLRRVYI PKASGKQRPL GIPTTKDRAM QALYALALEP VAETTADRNS Y GFRQGRCT ...String:
METRQMAVEQ TTGAVTNQTE TSWHSIDWAK ANREVKRLQV RIAKAVKEGR WGKVKALQWL LTHSFYGKAL AVKRVTDNSG SKTPGVDGI TWSTQEQKAQ AIKSLRRRGY KPQPLRRVYI PKASGKQRPL GIPTTKDRAM QALYALALEP VAETTADRNS Y GFRQGRCT ADAAGQCFTV LGRSDCAKYI LDADITGCFD NISHEWLLDN IPLDKEVLRK WLKSGFVWKQ QLFPTHAGTP QG GVISPML ANMTLDGMEE LLKKHLRKQK VNLIRYADDF VVTGESKETL EKVTTVIQEF LKERGLTLSE EKTKVVHIEE GFD FLGWNI RKYGEKLLIK PAKKNIKAFH KKIRDALKEL RTATQEAVID TLNPIIKGWA NYHRNQVSKR IFNRADDNIW HKLW RWAKR RHPNKPARWT KNKYFIKIGN RHWVFGTWKK DKEGRLRSRY LIKAGDTRIQ RHVKIKADAN PFLPEWAEYF EERKK LKEA PAQYRRIRRE LWKKQGGICP VCGGEIEQDM LTEIHHILPK HKGGSDDLDN LVLIHANCHK QVHSRDGQHS RFLLKE GL

UniProtKB: Maturase reverse transcriptase

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 51 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4r0d

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 87612
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 10 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4r0d


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6mec:
Structure of a group II intron retroelement after DNA integration

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